Biology subjects

Lee, S.

Publications and source records attributed to Lee, S..

At least 271 records · Page 15Linked to original sources

bioRxiv2024

Systemic and local chronic inflammation and hormone disposition promote a tumor-permissive environment for breast cancer in older women

Estrogen receptor positive (ER+) breast cancer is the most common subtype of breast cancer and is an age-related disease. The peak incidence of diagnosis occurs around age 70, even though these post-menopausal patients have low circulating levels of estradiol (E2). Despite the hormone sensitivity of age-related tumors, we have a limited understanding of the interplay between systemic and local hormones, chronic inflammation, and immune changes that contribute to the growth and development of these tumors. Here, we show that aged F344 rats treated with the dimethylbenz(a)anthracene / medroxyprogestrone acetate (DMBA/MPA) carcinogen develop more tumors at faster rates than their younger counterparts, suggesting that the aged environment promotes tumor initiation and impacts growth. Single-nuclei RNA-seq (snRNA-seq) of the tumors showed broad local immune dysfunction that was associated with circulating chronic inflammation. Across a broad cohort of specimens from patients with ER+ breast cancer and age-matched donors of normal breast tissue, we observe that even with an estrone (E1)-predominant estrogen disposition in the systemic circulation, tumors in older patients increase HSD17B7 expression to convert E1 to E2 in the tumor microenvironment (TME) and have local E2 levels similar to pre-menopausal patients. Concurrently, trackable increases in several chemokines, defined most notably by CCL2, promote a chronically inflamed but immune dysfunctional TME. This unique milieu in the aged TME, characterized by high local E2 and chemokine-enriched chronic inflammation, promotes both accumulation of tumor-associated macrophages (TAMs), which serve as signaling hubs, as well as polarization of TAMs towards a CD206+/PD-L1+, immunosuppressive phenotype. Pharmacologic targeting of estrogen signaling (either by HSD17B7 inhibition or with fulvestrant) and chemokine inflammation both decrease local E2 and prevent macrophage polarization. Overall, these findings suggest that chronic inflammation and hormonal disposition are critical contributors to the age-related nature of ER+ breast cancer development and growth and offer potential therapeutic insight to treat these patients. Translational SummaryWe uncover the unique underpinnings establishing how the systemic host environment contributes to the aged breast tumor microenvironment, characterized by high local estradiol and chronic inflammation with immune dysregulation, and show that targeting avenues of estrogen conversion and chronic inflammation work to restore anti-tumor immunity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/616978v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1ecd90borg.highwire.dtl.DTLVardef@9d7ac8org.highwire.dtl.DTLVardef@e7fb74org.highwire.dtl.DTLVardef@2da524_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Characterization of Newly Discovered Polyester Polyurethane-degrading Methylobacterium Aquaticum Strain A1

In this study, we present Methylobacterium aquaticum A1, a novel strain capable of degrading polyester polyurethane (PE-PUR). The attachment of M. aquaticum A1 to PE-PUR and its degradation capabilities were verified using Scanning Electron Microscopy (SEM) and Fourier-Transform Infrared Spectroscopy (FT-IR). Analysis of the reference genome of M. aquaticum revealed genes encoding enzymes with potential PE-PUR degrading activity, including esterases, lipase, proteases and amidase such as tesA, pgpB, aes, aprE, lon, degQ, and gatA. An esterase activity assay using p-nitrophenyl acetate (p-NPA) showed increased ester bond-cleaving activity when M. aquaticum A1 was exposed to polyurethane diol (PU-diol), suggesting inducible enzymatic activity involved in PE-PUR degradation. These findings highlight the potential of M. aquaticum A1 as a promising biocatalyst for PE-PUR degradation. IMPORTANCEMicrobial biodegradation is increasingly recognized as a sustainable approach to addressing microplastic pollution. This study introduces M. aquaticum A1, a newly isolated strain capable of adhering to and degrading polyester polyurethane (PE-PUR), one of the most widely utilized plastics. To our knowledge, this is the first report of PE-PUR degradation by a member of the Methylobacterium genus. This paper provides a detailed characterization of M. aquaticum A1 and identifies several enzyme candidates--tesA, pgpB, aes, aprE, lon, degQ, and gatA--as potentially involved in the degradation process. Given that Methylobacterium species are known to be ecologically beneficial and inhabit diverse environments, the capacity of M. aquaticum A1 to degrade PE-PUR presents a promising strategy for mitigating microplastic pollution across a range of ecosystems.

microbiology↗

bioRxiv2024

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

Age-related cognitive decline is associated with altered physiology of the hippocampus. While changes in gene expression have been observed in aging brain, the regulatory mechanisms underlying these changes remain underexplored. We generated single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D genome data from 40 human hippocampal tissues spanning adult lifespan. We observed a striking loss of astrocytes, OPC, and endothelial cells during aging, including astrocytes that play a role in regulating synapses. Microglia undergo a dramatic switch from a homeostatic state to a primed inflammatory state through DNA methylome and 3D genome reprogramming. Aged cells experience erosion of their 3D genome architecture. Our study identifies age-associated changes in cell types/states and gene regulatory features that provide insight into cognitive decline during human aging.

genomics↗

bioRxiv2024

Aβ-targeting synNotch Receptor for Alzheimer's Disease: Expanding Applications to Extracellular Protein Aggregates

The synthetic Notch receptor (synNotch) system is a versatile platform that induces gene transcription in response to extracellular signals. However, its application has been largely confined to membrane-bound targets due to specific activation requirements. Whether synNotch can also target extracellular protein aggregates, such as amyloid beta (A{beta}) in Alzheimers disease (AD), is unclear. To address this, we engineered an A{beta}-targeting synNotch receptor controlling the production of chimeric human-mouse versions of Lecanemab (Leqembi(R)) or Aducanumab (Aduhelm(R)), both FDA-approved antibodies for AD. We demonstrate that NIH 3T3 cells expressing this synNotch system detect and respond to extracellular A{beta} aggregates by synthesizing and secreting Aducanumab or Lecanemab. These findings broaden the potential applications of synNotch, extending its targets beyond membrane-bound proteins to extracellular protein aggregates, providing obvious benefits to research in this scientific arena.

synthetic biology↗

bioRxiv2024

Non-invasive brain-machine interface control with artificial intelligence copilots

Motor brain-machine interfaces (BMIs) decode neural signals to help people with paralysis move and communicate. Even with important advances in the last two decades, BMIs face key obstacles to clinical viability. Invasive BMIs achieve proficient cursor and robotic arm control but require neurosurgery, posing significant risk to patients. Non-invasive BMIs do not have neurosurgical risk, but achieve lower performance, sometimes being prohibitively frustrating to use and preventing widespread adoption. We take a step toward breaking this performance-risk tradeoff by building performant non-invasive BMIs. The critical limitation that bounds decoder performance in non-invasive BMIs is their poor neural signal-to-noise ratio. To overcome this, we contribute (1) a novel EEG decoding approach and (2) artificial intelligence (AI) copilots that infer task goals and aid action completion. We demonstrate that with this "AI-BMI," in tandem with a new adaptive decoding approach using a convolutional neural network (CNN) and ReFIT-like Kalman filter (KF), healthy users and a paralyzed participant can autonomously and proficiently control computer cursors and robotic arms. Using an AI copilot improves goal acquisition speed by up to 4.3x in the standard center-out 8 cursor control task and enables users to control a robotic arm to perform the sequential pick-and-place task, moving 4 randomly placed blocks to 4 randomly chosen locations. As AI copilots improve, this approach may result in clinically viable non-invasive AI-BMIs.

bioengineering↗

bioRxiv2024

Soil pH influences the composition of bacteriophage communities infecting individual hosts

Bacteriophages (phages) can infect a range of hosts in highly diverse soil bacterial communities. However, selection of host communities across ecological gradients and co-evolutionary processes may influence both the distribution of phages and the susceptibility of individual hosts through virus interactions and local adaptation within distinct ecological niches. Metagenomic-based analyses have revealed that soil pH selects for distinct populations and community structures for both phage and hosts at local and global scales. However, whether contrasting soil pH represents a selective barrier for phages capable of infecting an individual host is unknown. To examine the influence of pH on individual host-virus interactions, two closely related Bacillus strains were isolated and characterized from pH 7.5 soil associated with a long-term contiguous pH gradient (pH 4.5 to 7.5). Phages infecting each strain were subsequently enriched from soils across the pH gradient (pH 4.5, 5.5, 6.5 and 7.5), enumerated using a plaque assay, and characterized via metagenomic analysis. Phages infecting each strain were cultivated from all soils but their community composition and abundance varied with pH. Phage populations infecting each of the two strains were distinct despite the close relatedness of the two hosts, indicating relatively narrow host ranges for each virus. These results suggest that while phage community structures vary substantially across an ecological gradient, soil pH alone does not represent a barrier for the distribution of phages capable of infecting an individual host.

ecology↗

bioRxiv2024

Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia

INTRODUCTIONSex differences are apparent in neurodegenerative diseases, but have not been comprehensively characterized in frontotemporal dementia (FTD). METHODSParticipants included 337 adults with autosomal dominant FTD enrolled in the ALLFTD Consortium. Clinical assessments and plasma were collected annually for up to six years. Linear mixed-effects models investigated how sex and disease stage associated with longitudinal trajectories of cognition, function, and neurofilament light chain (NfL). RESULTSWhile sex differences were not apparent at asymptomatic stages, females showed more rapid declines across all outcomes in symptomatic stages compared to males. In asymptomatic participants, the association between baseline NfL and clinical trajectories was weaker in females versus males, a difference that attenuated in symptomatic participants. DISCUSSIONIn genetic FTD, females show cognitive resilience in early disease stages followed by steeper clinical declines later in disease. Baseline NfL may be a less sensitive prognostic tool for clinical progression in females with FTD-causing mutations.

neuroscience↗

bioRxiv2024

The Platinum Pedigree: A long-read benchmark for genetic variants

Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards often focus on specificity, neglecting completeness in difficult to analyze regions. To create a more comprehensive truth set, we used Mendelian inheritance in a large pedigree (CEPH-1463) to filter variants across Illumina, PacBio high-fidelity (HiFi), and Oxford Nanopore Technologies platforms. This generated a variant map with over 4.7 million single-nucleotide variants, 767,795 indels, 537,486 tandem repeats, and 24,315 structural variants, covering 2.77 Gb of the GRCh38 genome. This work adds [~]200 Mb of high-confidence regions, including 8% more small variants, and introduces the first tandem repeat and structural variant truth sets for NA12878. As an example of the value of this improved benchmark, we retrained DeepVariant using this data to reduce genotyping errors by [~]34%.

genomics↗

bioRxiv2024

Nanocluster-Mediated Signaling Crosstalk between FcγR and TLR4 in Macrophage Inflammatory Responses

Receptor crosstalk, the interaction between different receptors to modulate signaling, is crucial for fine-tuning the inflammatory responses of innate immune cells. Although the synergistic crosstalk between Toll-like receptor (TLR)4 and Fc gamma receptor (Fc{gamma}R) is well documented, the detailed mechanism underlying this synergy remains unclear. In this study, we addressed this knowledge gap by imaging the molecular organization of TLR4 and Fc{gamma}R on the macrophage cell surface and correlating it with their synergistic co-activation using ligands functionalized on lipid bilayers. We confirmed that co-activation of TLR4 and Fc{gamma}R enhances whole-cell pro-inflammatory responses and tyrosine phosphorylation at the receptor level. Super-resolution microscopy revealed that TLR4 and Fc{gamma}R each form discrete nanoclusters after ligand stimulation, and their synergistic co-activation significantly increases both the size and spatial overlap of these nanoclusters, leading to amplified immune signaling. Contrary to previous assumptions that TLR4 and Fc{gamma}R form heterodimers during their crosstalk, our results emphasize the critical role of receptor nanocluster interactions in modulating innate immune responses. Additionally, these findings align with similar receptor interaction mechanisms that we previously reported in other receptor pairs, such as Dectin-1/TLR2 and Fc{gamma}R/TLR2, suggesting that nanocluster interactions may represent a predominant mechanism governing crosstalk between TLRs and ITAM-containing receptors.

biophysics↗

bioRxiv2024

From Homogeneity to Heterogeneity: Refining Stochastic Simulations of Gene Regulation

Cellular processes are intricately controlled through gene regulation, which is significantly influenced by intrinsic noise due to the small number of molecules involved. The Gillespie algorithm, a widely used stochastic simulation method, is pervasively employed to model these systems. However, this algorithm typically assumes that DNA is homogeneously distributed through- out the nucleus, which is not realistic. In this study, we evaluated whether stochastic simulations based on the assumption of spatial homogeneity can accurately capture the dynamics of gene regulation. Our findings indicate that when transcription factors diffuse slowly, these simulations fail to accurately capture gene expression, highlighting the necessity to account for spatial heterogeneity. However, incorporating spatial heterogeneity considerably increases computational time. To address this, we explored various stochastic quasi-steady-state approximations (QSSAs) that simplify the model and reduce simulation time. While both the stochastic total quasi-steady state approximation (stQSSA) and the stochastic low-state quasi-steady-state approximation (slQSSA) reduced simulation time, only the slQSSA provided an accurate model reduction. Our study underscores the importance of utilizing appropriate methods for efficient and accurate stochastic simulations of gene regulatory dynamics, especially when incorporating spatial heterogeneity.

systems biology↗

bioRxiv2024

Intracortical injection of immune checkpoint inhibitor promotes monocyte/macrophage infiltration and restores microglial function and neuronal activity in an AD mouse model

Alzheimer's disease (AD) involves complex neuroimmune interactions. However, the role of immune checkpoint pathways in regulating the glial and neuronal functions of the AD brain remains unclear. This study aims to investigate how the brain-specific modulation of the PD-1/PD-L1 axis affects glial and neuronal function in an AD mouse model, which is characterized by the significant upregulation of microglial PD-1 and astrocytic PD-L1. A single intracortical administration of anti-PD-L1 antibody reshaped the glial microenvironment, which was accompanied by the restoration of impaired microglial process convergence. Astrocyte-specific Pd-l1 knockdown using the pSico system validated the essential role of astrocytic PD-L1 in enhancing microglial responses. Notably, the blockade of the PD-1/PD-L1 signaling pathway increased the microglial P2RY12 expression, a key marker of microglial homeostasis, which likely contributed to the restoration of neuronal hyperactivity. Collectively, these findings confirmed the potential of targeting the astrocyte-microglia PD-1/PD-L1 axis to mitigate AD pathology.

neuroscience↗

bioRxiv2024

A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner

We deployed the Blended Genome Exome (BGE), a DNA library blending approach that generates low pass whole genome (1-4x mean depth) and deep whole exome (30-40x mean depth) data in a single sequencing run. This technology is cost-effective, empowers most genomic discoveries possible with deep whole genome sequencing, and provides an unbiased method to capture the diversity of common SNP variation across the globe. To evaluate this new technology at scale, we applied BGE to sequence >53,000 samples from the Populations Underrepresented in Mental Illness Associations Studies (PUMAS) Project, which included participants across African, African American, and Latin American populations. We evaluated the accuracy of BGE imputed genotypes against raw genotype calls from the Illumina Global Screening Array. All PUMAS cohorts had R2 concordance [≥]95% among SNPs with MAF[≥]1%, and never fell below [≥]90% R2 for SNPs with MAF<1%. Furthermore, concordance rates among local ancestries within two recently admixed cohorts were consistent among SNPs with MAF[≥]1%, with only minor deviations in SNPs with MAF<1%. We also benchmarked the discovery capacity of BGE to access protein-coding copy number variants (CNVs) against deep whole genome data, finding that deletions and duplications spanning at least 3 exons had a positive predicted value of [~]90%. Our results demonstrate BGE scalability and efficacy in capturing SNPs, indels, and CNVs in the human genome at 28% of the cost of deep whole-genome sequencing. BGE is poised to enhance access to genomic testing and empower genomic discoveries, particularly in underrepresented populations.

genomics↗

bioRxiv2024

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes

Most phenotype-associated genetic variants map to non-coding regulatory regions of the human genome. Moreover, variants associated with blood cell phenotypes are enriched in regulatory regions active during hematopoiesis. To systematically explore the nature of these regions, we developed a highly efficient strategy, Perturb-multiome, that makes it possible to simultaneously profile both chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of a range of master transcription factors (TFs). This approach allowed us to examine the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within the TF-sensitive accessible chromatin regions, while representing less than 0.3% of the genome, show a [~]100-fold enrichment in heritability across certain blood cell phenotypes; this enrichment is strikingly higher than for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.

genomics↗

bioRxiv2024

Aquavert: Imaging and Microfluidics for Vertical Swimming of Microorganisms

Investigating aquatic microorganisms swimming and feeding behaviors under well-controlled conditions is of great interest across multiple disciplines. Thus, broader access to resources that enable these investigations is desirable. Given the organisms microscopic dimensions, an ideal system should combine microscopy to visualize and fluidics to control and modulate their environments. We report an integrated device (Aquavert) that combines DIY microscopy and microfluidics for biomechanical investigations of marine microorganisms, emphasizing vertical swimming. The DIY microscope was developed for modularity, and imaging chambers were secured in vertical orientations (either in portrait or landscape mode). Fluid channels were used to introduce flow and fluid segmentation while remaining upright. Fluid segmentation established two distinct environments (e.g., with and without algae) in neighboring regions inside a chamber. System application with multiple marine larvae (sand dollars, sea urchins, and starfish) and introduction of unicellular algae were demonstrated. Finally, the devices capabilities were extended to fluorescence imaging to visualize tracer beads. The role of gravity is often ignored in conventional plate or microfluidic experiments. Beyond the current application, Aquavert enables investigations of the behavior and physiology of microorganisms where the role of gravity is critical.

biophysics↗

bioRxiv2024

TRAIL receptor agonist TLY012 in combination with PD-1 inhibition promotes tumor regression in an immune-competent mouse model of pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) has an immunosuppressed, apoptosis-resistant phenotype. TLY012 is a pegylated recombinant Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL), an orphan drug for chronic pancreatitis and systemic sclerosis. Innate immune TRAIL signaling suppresses cancer. We hypothesized that combination of immune checkpoint-blocking anti-PD-1 antibody and TLY012 would have synergistic anti-tumor efficacy in immune-competent PDAC-bearing mice. PDAC tumor-bearing C57Bl/6 mice treated 10 mg/kg anti-mouse PD-1 antibody twice weekly and 10 mg/kg TLY012 three times weekly had reduced tumor growth and tumor volume at 70 days compared to either drug alone (all p<0.005). B-cell activating factor (BAFF), which promotes PDAC tumors, decreased to 44% of control mice with dual treatment at 7 days and remained decreased at 3 months. Long-term dual treatment showed the highest levels of proinflammatory cytokines interferon gamma (average 5.6 times control level, p=0.046), CCL5 (average 14.1 times control level, p=0.048), and interleukin-3 (IL-3, average 71.1 times control level, p=0.0053). Flow cytometry showed trends toward decreased circulating regulatory T cells, increased NK cells, and a higher proportion of CD8+ T cells within tumors in dual treatment group. In summary, combination of anti-PD-1 and TLY012 prevented growth of PDAC in an immunocompetent mouse model while increasing tumor-infiltrating CD8+ T cells, decreasing circulating T-regulatory cells and altering cytokine expression of CCL5, interferon gamma and IL-3 to promote proinflammatory, antitumor effects. Combining TLY012 and anti-mouse PD-1 creates changes in immune cell and cytokine levels to induce a more proinflammatory immune environment that contributes to decreased PDAC tumor growth.

cancer biology↗

bioRxiv2024

The gut microbiota is a determinant of sexual dimorphism in ALS-linked TDP43 mice

The mechanisms underlying the earlier onset and male predominance of amyotrophic lateral sclerosis (ALS), the most common form of human motoneuron disease, are poorly understood. Here we show that the gut microbiota protects against TDP43 toxicity and contributes to the sexual dimorphism in mice expressing a mutant form of TDP43 (A315T) linked to ALS. TDP43 mice raised under germ-free conditions, or treated with antibiotics to deplete the gut microbiota, develop motoneuron disease earlier and show no sex differences in onset and lifespan. Behavioral and histopathological analyses confirm the exacerbation in neurodegeneration caused by the absence of gut microbiota. Castration did not alter disease course of male TDP43 mice, suggesting that male sex hormones do not interact with the gut microbiota to confer disease phenotype. Future identification of gut bacteria species and their mechanisms of action offers a unique opportunity to understand sexual dimorphism in ALS, with the ultimate goal to develop non-invasive and sex-specific treatments for ALS.

physiology↗

bioRxiv2024

Normalization of Single-cell RNA-seq Data UsingPartial Least Squares with Adaptive Fuzzy Weight

Normalization of single-cell RNA-seq (scRNA-seq) is a crucial step in downstream analysis, where raw data are adjusted to correct unwanted factors that prevent the direct comparison of expression measures. scRNA-seq data exhibits a multivariate relationship between transcript-specific expression and sequencing depth that a single scale factor cannot address. A partial least squares (PLS) regression was performed to accommodate the variability of gene expression in each condition, and upper and lower quantiles with adaptive fuzzy weights were utilized to correct unwanted biases in scRNA-seq data. The present approach was compared using real and simulated datasets across various state-of-the-art performance measures.

bioinformatics↗

bioRxiv2024

Structure and function of the human apoptotic scramblase Xkr4

Phosphatidylserine externalization on the surface of dying cells is a key signal for their recognition and clearance by macrophages and is mediated by members of the X-Kell related (Xkr) protein family. Defective Xkr-mediated scrambling impairs clearance, leading to inflammation. It was proposed that activation of the Xkr4 apoptotic scramblase requires caspase cleavage, followed by dimerization and ligand binding. Here, using a combination of biochemical approaches we show that purified monomeric, full-length human Xkr4 (hXkr4) scrambles lipids. CryoEM imaging shows that hXkr4 adopts a novel conformation, where three conserved acidic residues create an electronegative surface embedded in the membrane. Molecular dynamics simulations show this conformation induces membrane thinning, which could promote scrambling. Thinning is ablated or reduced in conditions where scrambling is abolished or reduced. Our work provides insights into the molecular mechanisms of hXkr4 scrambling and suggests the ability to thin membranes might be a general property of active scramblases.

biophysics↗